Variant rs4054823 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.426 in 151,954 control chromosomes in the GnomAD database, including 14,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14141 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64739

AN:

151836

Hom.:

14130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.463

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.426

AC:

64789

AN:

151954

Hom.:

14141

Cov.:

AF XY:

0.431

AC XY:

31998

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.319

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.463

Gnomad4 EAS

AF:

0.524

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.493

Gnomad4 NFE

AF:

0.457

Gnomad4 OTH

AF:

0.421

Alfa

AF:

0.449

Hom.:

21867

Bravo

AF:

0.419

Asia WGS

AF:

0.485

AC:

1688

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over